A global Earth System model is employed to investigate the role of direct temperature effects in the response of marine ecosystems to climate change. While model configurations with and without consideration of explicit temperature effects can reproduce observed current biogeochemical tracer distributions and estimated carbon export about equally well, carbon flow through the model ecosystem reveals strong temperature sensitivities. Depending on whether biological processes are assumed temperature sensitive or not, simulated marine net primary production (NPP) increases or decreases under projected climate change driven by a business‐as‐usual CO₂ emission scenario for the 21st century. This suggests that indirect temperature effects such as changes in the supply of nutrients and light are not the only relevant factors to be considered when modeling the response of marine ecosystems to climate change. A better understanding of direct temperature effects on marine ecosystems is required before even the direction of change in NPP can be reliably predicted.